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... Green on blue is modeled after an earlier phrase, blue on blue, referring to inadvertent clashes between members of the same side in an armed conflict... Blue on blue originated in the British military in the early 1980s, but has now spread around the world, and even moved beyond the military sphere to describe accidental shootings among police officers.

What are the blue and green referred to in these phrases? It doesn’t have anything to do with uniforms. The formulation is based on the standardized military symbols used to indicate different forces on maps. In this system, the color blue is used for friendly forces, red for hostile forces, green for neutral forces, and yellow for unknown forces. Thus, blue-on-blue shootings are incidents in which members of the same force fire on one another.

What green on blue means is a bit more complicated. In addition to Afghanistan, green on blue has also been used in the context of Iraq; US General Raymond Odierno referred to the threat of “green-on-blue attacks” by Iraqi security forces on US personnel in Iraq in 2009 (Politico, 28 May). It would seem that in the context of the Iraq and Afghanistan, the local security forces are regarded as neutral, or green: not hostile, but not fully allies, either.

The phrase "green on blue" originates from the colour assignments for the various forces in a theatre of operations as shown in the tactical displays. These displays are now all electronic, but this holds true for older systems of markers on paper maps as well.

Red traditionally signifies danger, and is therefore used to show the enemy.
Both green and blue were used for friendly forces in the past. However, with the proliferation of UN "peacekeeping" missions in the 1970s and 80s, the blue was used more for UN forces. This is because UN troops always wear a bright blue helmet or beret due to the UN needing to have it's forces clearly recognizable as UN rather than any one nation. UN vehicles are usually white with the letters UN marked on them, for the same reason.

From this, "green on blue" has come to mean "friendly forces firing on the foreign international peacekeepers".